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config-haddock3.yaml
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config-haddock3.yaml
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# Example configuration file for haddock3 and haddock3-re.
# Expects executables to be in PATH,
# if not edit this file to use absolute path to executables
job_root_dir: jobs
destination_picker: bartender.picker:pick_first
applications:
haddock3:
command_template: haddock3 workflow.cfg
upload_needs:
- workflow.cfg
runimport:
summary: Import a HADDOCK3 run.
description: >
Upload an archive of haddock3 output.
The archive should have run dir as root.
The run should have haddock3-clean and haddock3-analyse executed on it.
command_template: mkdir -p output && mv * output || true
# Below are other haddock3 commands,
# that could be hosted by bartender web service.
# haddock3-pp:
# summary: HADDOCK3 preprocess PDB files
# command_template: haddock3-pp --output-directory . *.pdb
# haddock3-analyse:
# command_template: haddock3-analyse --run-dir . -m {{ modules|q }}
# input_schema:
# additionalProperties: false
# type: object
# properties:
# modules:
# type: string
# description: List of module numbers to analyse. Space separated.
destinations:
local:
scheduler:
type: memory
slots: 1
filesystem:
type: local
interactive_applications:
rescore:
command_template: >
haddock3-re score
--w_elec {{w_elec|q}} --w_vdw {{w_vdw|q}} --w_desolv {{w_desolv|q}} --w_bsa {{w_bsa|q}} --w_air {{w_air|q}}
{{ capri_dir|q }}
&&
haddock3-analyse --is_cleaned True --inter True -m {{ module_nr|q }} -r output/
description: Rescore a HADDOCK run with different weights.
input_schema:
additionalProperties: false
properties:
module_nr:
type: number
capri_dir:
type: string
w_air:
type: number
w_bsa:
type: number
w_desolv:
type: number
w_elec:
type: number
w_vdw:
type: number
required:
- module_nr
- capri_dir
- w_elec
- w_vdw
- w_desolv
- w_bsa
- w_air
type: object
reclustrmsd:
command_template: >
haddock3-re clustrmsd --plot_matrix
{% if criterion == 'maxclust' -%}
--n_clusters {{n_clusters|q}}
{% else -%}
--clust_cutoff {{clust_cutoff|q}}
{% endif -%}
{% if min_population -%}
--min_population {{min_population|q}}
{% endif -%}
{{clustrmsd_dir|q}}
&&
haddock3-analyse --is_cleaned True --inter True -m {{ module_nr|q }} -r output/
description: Recluster a HADDOCK run with RSMD and different parameters.
input_schema:
additionalProperties: false
properties:
module_nr:
type: number
clustrmsd_dir:
type: string
criterion:
type: string
enum: [maxclust, distance]
clust_cutoff:
type: number
n_clusters:
type: number
min_population:
type: number
required:
- module_nr
- criterion
- clustrmsd_dir
type: object
reclustfcc:
command_template: >
haddock3-re clustfcc --plot_matrix
--clust_cutoff {{clust_cutoff|q}} --strictness {{strictness|q}} --min_population {{min_population|q}}
{{clustfcc_dir|q}}
&&
haddock3-analyse --is_cleaned True --inter True -m {{ module_nr|q }} -r output/
description: Recluster a HADDOCK run with FCC and different parameters.
input_schema:
additionalProperties: false
properties:
module_nr:
type: number
clustfcc_dir:
type: string
clust_cutoff:
type: number
strictness:
type: number
min_population:
type: number
required:
- module_nr
- clustfcc_dir
- clust_cutoff
- strictness
- min_population
type: object